[English] 日本語
Yorodumi
- PDB-7nhz: NMR structure of Rv1813c from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nhz
TitleNMR structure of Rv1813c from Mycobacterium tuberculosis
ComponentsUncharacterized protein Rv1813c
KeywordsAPOPTOSIS / metabolism / mitochondria / effector
Function / homologyDomain of unknown function DUF4189 / Domain of unknown function (DUF4189) / Uncharacterized protein Rv1813c
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsBarthe, P. / Cohen-Gonsaud, M.
CitationJournal: To Be Published
Title: A Mycobacterium tuberculosis effector targets mitochondrion, controls energy metabolism and limits cytochrome c exit.
Authors: Cohen-Gonsaud, M. / Barthe, P. / Mukamolova, G.V.
History
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein Rv1813c


Theoretical massNumber of molelcules
Total (without water)12,7141
Polymers12,7141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8550 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein Rv1813c


Mass: 12714.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1813c, MTCY1A11.30, MTY16F9.01 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WLS1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-15N TOCSY
132isotropic13D HNCA
142isotropic13D CBCA(CO)NH
152isotropic13D HN(CA)CB
162isotropic13D HNCO
172isotropic13D HN(CA)CO
183isotropic12D NOESY
193isotropic12D TOCSY
1103isotropic12D DQF-COSY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM [U-15N] Rv1813c, 90% H2O/10% D2Owith 25 mM NaCitrate15N_sample90% H2O/10% D2O
solution20.9 mM [U-13C; U-15N] Rv1813c, 90% H2O/10% D2Owith 25 mM NaCitrate13C_sample90% H2O/10% D2O
solution30.8 mM Rv1813c, 100% D2Owith 25 mM NaCitrateD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRv1813c[U-15N]1
0.9 mMRv1813c[U-13C; U-15N]2
0.8 mMRv1813cnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 5.6 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CINDYPadillachemical shift assignment
GifaDelsucpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: RECOORD procedure
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more